Story of Hybrids
by Ahopindarkness
Summary: When a girl is nearly killed, she learns that she has powers of Pokemon. Hunted by Team Rocket, she must band together with other children like her and learn how to use her gifts. T to be safe.
1. Chapter 1

_I do not own Pokemon and if I did, this wouldn't be here._

_Warning: I am a procrastinator._

_I should hopefully get a chapter done every two weeks, but see note above._

* * *

Chapter 1

The red-headed girl didn't seem that out of the ordinary. It was strange, of course, that she was walking with such fierce determination in her eyes down what was probably the dirtiest, darkest, most crime-ridden part of whatever city she happened to be in.

Giovanni concluded that she was either a reckless runaway, a lunatic, or downright suicidal. It hardly mattered. So it barely surprised him when a thirty-something looking man clutching an empty bottle of some kind of alcohol stood in her way and muttered something incomprehensible.

The girl stopped in her tracks, her eyes burning in rage, seeming to dare the man to approach. He started toward her with a groping hand outstretched. She easily sidestepped out of the way. The man grew frustrated and clumsily swung his glass bottle at his victim. The girl managed to duck but received a kick instead. She was flung forward, but managed to land in a roll and crouch, barely preventing her head from basking against the alley walls. In her crouch, the girl bellowed in wrath. A mass of flames formed in her palms and her eyes grew red, literally.

This was what Giovanni was waiting for. As the screen continued on to show the man falling to the filthy ground in shock and the girl making her escape, Giovanni asked in a calm, controlled voice, "Is there any way this could be a fraud?"

Prof. Haban stood up, his beady eyes darting around under his thick, protruding eyebrows. "That's what I thought at first, but after the other reports I have reason now to believe it's legit."

"Show me the other tape."

The screen flashed to life again, this time showing a shaky hand holding a camera. The hidden figure ran through a sparse forest chasing a boy with jet black hair holding a young, frightened little girl by her arm.

Giovanni studied the boy, a healthy-looking twelve-year old, just like the girl in the alley. They a clearing, and suddenly he too was surrounded by a strange aura. Wings covered with feathers as black as the boy's hair sprouted on the boys back. He scooped the little girl into the arms soared into the air, the camera's holder shaking harder than ever before. "Oh my Arceus," smattered a feminine voice from the video, "Arceus, o my Arceus"

The screen went blank again.

Prof. Haban said, "And then there's this case. I saw it happen with my own eyes, well not exactly saw it happen in person per say but I saw its results. A student at Hartmond Pokémon Prep Public School, the Pokémon school I teach at, you know as a cover-up. Well there was this student his name was Brian, a rather brawny young lad though rather suspicious in my opinion. Well he shoved another pupil into the wall and broke his ribs, not Brian's but the other student's, who – "

Giovanni rolled his eyes. "Cut to the chase."

Prof. Haban cleared his throat. "Well sir, as I was saying, there were cracks in a solid, concrete wall. No one should be able to do that, much well a young boy." He shifted nervously on his feet. "I, Sir, instantly though of the old experiment 19 in the Genetics Department. Could it be, I mean could it be possible – Sir, are you sure the hybrid embryos were actually destroyed

Giovanni collapsed to his chair and closed his eyes. _Those hybrids, they were supposed to be disposed of after Mewtwo escaped. These children are the age we estimated they would begin to show powers. _

Giovanni stood up. "This is of upmost importance. Look into everything you can find about children doing seemingly impossible feats. I mean everything. If you find something, immediately tell me. Also give these orders to Prof Fuji, Dominique –"

* * *

Jonathan had heard enough. Dangling near an open vent, he silently crawled back. In a few minutes he came to a room where her friend Amy was waiting. Her blonde curls bouncing up and down, the thirteen year old girl asked, "Well Jonny, did you learn anything?"

Jonathan replied, "Yes, but we need to get out as soon as possible. Are the guards still out?"

"Still out cold, I guess I shocked them a little too hard. I also shut off the security cams, but they will probably be able to reload the system and see us come in."

He nodded, "Good, let's hurry and get out, I'll tell you what I heard outside." The boy and girl scrambled away, leaving the empty security room of this Rocket hideout.

* * *

About an hour later, Giovanni watched the security cam recording. It showed two children; a girl one tall with rosy cheeks and blonde hair, and a male one that was both small and skinny with closely cropped olive hair. As they barged into the security room, the blonde sent sparks at the guards, knocking them out cold. The puny one produced web out of his hand, tying them up and shoving them in a closet nearby.

At the end, Giovanni clenched his fists. He wanted those mutants in his possession; there was no time to waste.

* * *

Jonathan sat down in his room in the orphanage for what was probably going to be for the last time. All in all, his and Amy's sort of secret mission went rather well, except for the fact that a surprised guard had grazed him in the arm with his gun.

He remembered that interesting chat he had with Mrs. Julson about that injury, coupled with his being absent from school, on the day he was to receive his first Pokemon no less.

Finally, someone knocked out the door. Amy burst into the room and asked, "Anyone else here?" She looked around and answered herself. "I guess not." Her ever present smile reemerged. "So, Jonny, now that we know what has been going on lately, what should we do? Maybe get some Pokémon and travel all around Johto as a wall-climbing superhero with his staticy sidekick."

Jonathan wondered how Amy could be so positive in a time like this. Personally, Jonathan was afraid his head might explode. "I am not quite sure Amy. Well obviously we got to get away from here now that Team Rocket knows who we are." They really should have thought this through. He closed his eyes and thought. After a few moments silence, he said with what he hoped was conviction. "There are others like us. Like the people we sure Giovanni and that nervous professor person talking about. We need to find them and maybe join up with them and definitely know what's going. There's just no way we can keep hiding our gifts any longer."

Amy nodded, still happy looking but serious too. "All I know," she said in a determined whisper, "is that wherever you go, I go. Let's do this, Jonathan."

"I guess we should leave tonight. Let's wait until nightfall and then sneak out. I guess we're camping in the woods tonight."

"Yeah, we better leave before they figure where we are."

"Unless" he said, "they are already know we're at this orphanage."

Amy threw a pillow at him, "You really are paranoid sometime, Jonny."

Jonathan tried his best to act normal at dinner. Since Amy lived at a girl's orphanage and he at a boy's orphanage, he was alone. As he absent mindedly fiddled with the broccoli on his plate, he wondered what she was doing right now, if she was safe. Maybe Team Rocket had already got her. But no, Team Rocket seemed to want to keep this a secret. It wouldn't make sense for them to launch an attack, on orphanage of all things. _That _would certainly raise questions. They don't even do things like that anyway. They just work as independent units that steal other people's Pokemon and rob stores and other criminal stuff like that. Of course, there was always a first for everything . . .

Jonathan later wondered how he ever got through the evening.

Jonathan and Amy met outside. Neither of them were technically supposed to be out after curfew, but managed to escape anyways. Jonathan had it easy – all he had to do was climb out the window and crawl like an Ariados down the wall once he had made sure everyone who shared his room was sleeping. Amy had a tougher time. She tried to jump out the window onto the branches of a nearby tree. She was able to hook onto a branch, but barely. By the time Jonathan arrived she was dangling from a branch about 9 feet off the ground by her hands and struggling to get onto the branch.

After helping her down, the two snuck up the orphanage ground and across the dark and deserted town. Neither of them talked as they walked, not even Amy, who would usually be talkative and bubbly at such excitement. They decided not to not to get a Pokemon, even though they

were supposed to have gotten three of them in class today. A full team's worth of missing Pokemon would give them even more attention than they would doubtlessly get when people realized they were missing in the morning.

Amy yanked on Jonathan's shoulder. "A car!" she hissed. Two glowing points of light were heading towards them. They frantically looked around and ducked into a nearby alley and behind a dumpster. They heard rumbling of not just one, but several vehicles in quick succession.

They waited a few minute after they heard the last car drive away. All was quiet. Jonathan stepped out from their hiding place and looked around. "It's all clear." His whisper penetrated the silence.

They both stepped back from the alley to the sidewalk. Amy whispered. "There's got to be a reason all these people are out."

Jonathan closed his eyes and nodded solemnly. He instantly thought of all his friends at home. Why did he have to go and add sneak into the Rocket base anyway? They were being careless, reckless, idiotic even. If they hadn't snuck into the base, Team Rocket wouldn't even know about them. Then at dinner he wouldn't have been worrying about the future. He would have been fine, happy! He just missed his chance to get a Pokemon of his very own for crying out loud! What was he doing? Now his life, and Amy's, was in danger.

He shook his head. No. There use crying over spilled milk. He thought about the others. The other kids who were like him and Amy. Now he had learned a bit more about he was, not that it exactly reassured him.

"Hey, Jonny, you okay?"

Jonathan stopped moving. He hadn't even realized he had been walking; his feet had just mechanically begun to follow Amy. Now they were at the outskirts of the Ilex Forest.

Jonathan gazed into the towering trees of the Ilex Forest, dense enough to block out any sunlight if it wasn't the dark of night. "We'll have to walk all night. In the morning we'll get our sleep." Jonathan dreaded the long night ahead.

"That seems rather backwards, doesn't it?" quipped Amy. Jonathan looked at her face in the dim moonlight. She was smiling, exuberance oozing out every pore of her body. Again, how could she be so happy at a time like this?

As if in answer to his thoughts, she said, "This is the adventure everyone always dreams of, a chance to go off into the unknown and be heroes."

She beamed. "I don't suppose you've been considering going around as a wall – climbing superhero, eh Jonny?"

Jonathan smiled, "As long as you're my staticy sidekick"

Amy held onto his hand.

As an afterthought, Jonathan said, "Oh, and call me Peter now. Just to be safe."

Amy laughed. "Okay, Peter Parker, here we go."

* * *

_Notes: This is actually a prolouge of sorts. Amy and Jonathan/Peter are going to be only supporting roles and next chapter the real main characters will be introduced. _

_Also, this was a Nanowrimo novel (only got two chapters done though) so one of the big problems is that it is too wordy in places. And I want to make it clear that Amy and Jonathan are not boyfriend/girlfriend, though I do realise it would seem that way to some people. And as to why they went to the Team Rocket Hideout on that particular day and that particular time, I think that they overheard people talking or something. Just ignore it. Lastly, I actually wrote this and published it to the site a while ago, but then I got too busy to continue it. _


	2. Chapter 2

Chapter 2

Getting her first Pokémon was supposed to be the greatest thing that was supposed to happen in her childhood. Of course, Emily ought to have known that with her rotten luck nothing could be that easy. She sighed and put her pokeball back onto the belt around her waist. Most everyone else had their Pokémon that they had receive three weeks ago out. Emily would be too embarrassed to send hers out. That, and she would be in fear for her life.

Really, why did it have to be her? Why couldn't she have gotten nice, normal Pokémon like everyone else? Well, she knew why. Unlike most people, Emily's guardians didn't pay for her Pokémon school. You didn't actually have to give any money, but if you did, depending on how much you paid, you got better, rarer Pokémon. If you didn't pay, you just got the basics; a starter Pokémon of your choice, a Sentret or a Rattata, and a Pidgey or a Hoothoot. She really didn't care which kind of Pokémon she got as long as she got one. Of course, she didn't realize that if you don't pay you also got the hardest Pokémon to work with, which was in her case practically impossible.

The bell rang, signaling for all students to return to class. Most of the people returned their Pokémon into their pokeballs, but some kept theirs out even though the bell also meant that all Pokémon should be returned. Those that kept those out were mostly the ones whose parents had paid a lot of money for their schooling. Those kids had exotic Pokémon, like Staru, Lickitungs, and even a Dragonini, the only dragon type naturally found in the Johto and Kanto regions.

Emily was almost to the classroom and most of the kids had withdrawn their Pokémon, except one. A boy named Lucas Perry still had his Growlithe out. The red, bushy – tailed dog Pokémon stood near its master's feet, looking curiously up at Lucas's arrogant face. The Growlithe looked around the room and at seeing it was left the only left out it gave its master a soft, concerned bark. Lucas ignored his Pokémon however, and crouched down and whispered in its ear.

Emily looked at the Growlithe's face. The Pokémon looked torn. It backed away a couple steps away and gave another bark that said, seemed to say, "No."

Lucas grew angry but upon hearing the teacher's footsteps hastily returned the Growlithe to her ball. The teacher, Mr. Stoch, entered the classroom. "Everyone take a Pokémon, just one, out of its Pokeball please."

"Oh great," Emily muttered under with breath. She looked at her pokeballs and thought about which Pokémon to send out. Her Sentret was actually a lot stronger than other Sentret, but it never did anything. And her Cyndaquil . . . no, definitely not Cyndaquil.

She eventually decided to send out her Pidgey - Emily thought that it at least tried to be a good Pokémon. The small tan – feathered bird was released and it blinked in the bright sunlight the shone through the sparkling clean windows.

Mr. Stroch gestured with an elaborate movement of his hands. "All students shall proceed to the battle arena outside of the school house building." He commanded with a dreamy tone of voice.

Emily's Pidgey, which was nicknamed Atlanta by the Pokémon Prep School, was gazing at the window and absent – mindedly fluttering its silky soft feathers. "Come on, Atlanta." Everyone else with their Pokémon were already shuffling out the door to the fresh air outside.

Only after Emily gently placed a hand on its wing joint was Atlanta shaken out of its reverie. She gave an apologetic chirp and quickly fluttered into the air with a few hasty flaps of its wing and glided out the door, barely missing its frame.

Mr. Stoch gave another absent wave of his arms and said, "Everyone pair up and have your Pokémon do a mock battle. Under no circumstances should any of you student give serious damage to your opponent's Pokémon, your opponent, or myself." He glared at a few of the boys in the class, including Lucas. "Understand? I will be watching. Begin."

"Want to pair up with me, Emily?' Lucas asked in a perfectly innocent and polite tone of voice. Emily didn't trust him, for good reason. Unfortunately, everyone else had already found a partner and Lucas was the only one left.

"Get to a practice arena, Mr. Perry and Miss Starkwell," she heard Mr. Stoch say. Left with no other choice, she grudgingly nodded and went other to a challenger box in the remaining practice arena. With a triumphant smile, he asked curiously, "Hey, Emily, where's your Pokémon?"

Her heart dropping, Emily looked anxiously around and spotted Atlanta flitting around aimlessly again. "Atlanta!" she called, concealing a groan. Lucas snickered. The Growlithe was standing in the arena, its head cocked. She let out a half bark half growl. In a subconscious part of her mind, Emily registered that it meant, "Be careful."

Lucas ordered, "Circe, use ember!" Atlanta wasn't even in the arena yet. The small bird Pokémon frantically swerved out of the path of the flames and lost ground quickly and crashed onto the hard packed earth.

"Go. Use scratch!"

"Don't try getting up, Atlanta. Use sand attack!"

Fine grains of sediment were flung in the canine eyes, causing the Growlithe stop in its tracks and shield its eyes. Atlanta flew up towards Lucas's side of the arena, wings flapping frantically.

Emily called out her first attack. "Use scratch." At the same time Lucas smirked. "Ember."

Atlanta managed to dodge the attack and scrambled in the air again. It soared way off course off the arena. As it plummeted to the ground, Emily ran over to her fallen Pokémon.

"If your Pokémon has fainted please send out your next one," called out Mr. Stoch as he hustled over to a girl who was trying to get her Chikorita to use Frenzy Plant.

Emily gritted her teeth as she returned Atlanta. "Come out Agamemnon!" A Sentret appeared.

"Come on, Circe, use bite!"

"Use Quick Attack!" Emily added silently, "Please"

Of course, Sentret could do no such thing and decided a halfhearted Growl attack would work much better. Hardly daunted, the Growlithe tried to sink its teeth into Agamemnon, but the Pokémon skipped nimbly out of the way and Circe's canines only grazed the tips of Sentret's tail. Sentret gave out a screech and collapsed dramatically onto the ground, not even bothering to conceal its grin.

Lucas's voice has cracked with laughter. "You better send out your next Pokémon, this one has fainted."

Emily wanted to bang her head against a brick wall as she returned Sentret. She reluctantly unclipped the Pokeball and called out her last Pokémon, her starter, Theseus.

Emily's body tensed as the Cyndaquil looked around then focused its gaze on her. For a stubby-limbed, timid-eyed Pokémon, it did a darn good job looking murderous. "Theseus, we are in a battle here. Please use Scratch on that Growlithe."

But the Growlithe was already charging at Theseus. Theseus casually turned it head and looked calmly on its oncoming assailant. Just as it was about to be run over by a mass of teeth and claws, it suddenly jumped out of the way and let out an ember at Circe's rear end.

Circe yelped in irritation and surprise as the flames nipped at her. Lucas ordered her to attack again, but the same thing again occurred. Growlithe attacked, Theseus dodged and then used Ember. All in all, the battle was going better than Emily had hoped – Lucas was beginning to look nervous – but Theseus's Ember attacks did not do much more than annoying Growlithe. Eventually the Fire Dog Pokémon would be able to get in a move.

Emily spoke up in as passive a voice she could muster, "Um, good job Theseus, but maybe you could try using Scratch," hoping she was not making a mistake. She was making a mistake.

At Emily's command Theseus without turning around glared at its trainer. Circe the Growlithe was panting because of all the battling it had done, but other than that, it showed no sign of any damage.

Lucas yelled, "Come on, get it with Bite already!"

The exhausted Pokémon charged again, fangs bared. Theseus had no trouble dodging and it ran away toward Emily's side of the field. Growlithe face planted on the ground. As Lucas tried to order his Pokémon to get up Theseus charged another Ember more powerful than the previous, the flames on its back raging madly. The Ember was let loose. Some crashed against Circe, but Theseus whirled around creating an ascending arc of fire, and the brunt of the attack was launched at Emily's face.

Though Emily has only a split second to see it coming, she somehow managed to lunge to the left in time to avoid her Pokémon's attack. Lying on the grass facedown, soon Emily couldn't feel the flame's heat to the side of her anymore. She sat up. Theseus's attack luckily did not catch anyone, but everyone was staring at her. Lucas was just gaping at her with a shocked expression and Theseus wore a brooding expression – probably because he missed. After doing a quick mental check of all her body parts, she thought for a moment that she was escaped completely unharmed. Then she was aware of Mr. Stoch gesturing wildly and yelling, "Miss Starkwell your hair!"

A part of Emily's light brown hair was burning. A frazzled girl "helpfully" had her Totodile use Water Gun to help put it out.

Mr. Stoch walked over as the Totodile girl tried to apologize and said. "Er, well, I suppose your battle is over now."

* * *

Emily obviously did not score well on the practice battle. Because the only Pokemon he used still had a lot of HP left at the end of the battle, Lucas scored very well. "Thanks, Emily, I couldn't have done it without you!" he cheerily said after he received his marks.

At the end of the day Emily trudged outside. She did not have her Pokémon out.

Lucas was talking amidst a group of his friends. "- with Emily if you want a good grade. _Everyone _is good compared to her." Emily glared at them. As they were walking, Lucas apparently tripped over his own feet, toppling into a few of his companions. Emily smiled inside and thought, "At least something good happened today."

* * *

Gabriel squinted at the girl. It was gone now, but he could have sworn he had seen something around her. It wasn't very clear, probably no one else could see it, but with his eyesight it was noticeable.

Holding his backpack in his hand, he walked over to get a closer look. "Excuse me," he said. The girl turned around, revealing a fair-skinned face and blue eyes. "um… do you know where the Pokémon Center is?"

She nodded and told him. While she answered, Gabriel looked at, studied, and memorized her face. He heard himself say, "Thank you," and walked in the direction she had told him the PokeCenter was."

"Excuse, do you know that there are holes in the back of your shirt?" the girl said from behind him.

Gabriel cursed himself mentally.

Outside he just shrugged and put his on his backpack without turning around, "I know."


End file.
